SMTL ID : 2iwh.1

Structure of yeast Elongation Factor 3 in complex with ADPNP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-dimer

Ligands

2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.1: 14 residues within 4Å: Chain A: I.47, E.48, H.49, D.50, S.88, P.394, T.397, I.398, H.401, E.402, N.708, E.927, N.930, H.956 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:I.47, A:H.49, A:D.50, A:T.397, A:E.402, A:E.402, A:E.927, A:N.930, A:H.956 Salt bridges: A:H.49, A:H.401 pi-Stacking: A:H.49 ANP.7: 16 residues within 4Å: Chain B: I.47, E.48, H.49, D.50, S.88, P.394, T.397, I.398, H.401, E.402, N.708, E.927, N.930, H.956, S.957, E.959 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:E.48, B:H.49, B:D.50, B:D.50, B:T.397, B:E.402, B:E.402, B:E.927, B:E.927, B:N.930, B:H.956, B:E.959 Salt bridges: B:H.49, B:H.401

12 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 5 residues within 4Å: Chain A: S.550, G.551, G.552, W.553, N.583 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.550, A:G.552, A:N.583 SO4.3: 4 residues within 4Å: Chain A: K.453, Q.455, K.622, R.624 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.453, A:Q.455 Salt bridges: A:K.622, A:R.624 SO4.4: 4 residues within 4Å: Chain A: V.588, N.589, N.592 Chain B: R.877 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:N.589, A:N.592 Salt bridges: B:R.877 SO4.5: 6 residues within 4Å: Chain A: N.470, G.471, C.472, G.473, K.474, S.475 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.471, A:C.472, A:G.473, A:K.474, A:S.475 Salt bridges: A:K.474 SO4.6: 5 residues within 4Å: Chain A: Y.660, E.662, G.663 Chain B: T.524, E.526 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.660, A:E.662, A:G.663 SO4.8: 4 residues within 4Å: Chain B: T.265, I.306, A.307, D.308 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:A.307, B:D.308 SO4.9: 3 residues within 4Å: Chain B: S.550, W.553, N.583 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.550, B:N.583 SO4.10: 6 residues within 4Å: Chain B: P.469, G.471, C.472, G.473, K.474, S.475 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:G.471, B:C.472, B:G.473, B:K.474, B:S.475 Salt bridges: B:K.474 SO4.11: 3 residues within 4Å: Chain B: P.421, V.422, G.423 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.422, B:G.423 SO4.12: 7 residues within 4Å: Chain A: T.524 Chain B: Y.660, L.661, E.662, G.663, V.664, K.665 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Y.660, B:G.663, B:V.664, A:T.524 SO4.13: 4 residues within 4Å: Chain A: E.526 Chain B: V.664, K.665, L.698 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.526 SO4.14: 5 residues within 4Å: Chain B: D.609, N.629, T.631, H.896, R.898 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.629, B:T.631 Salt bridges: B:R.898

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Andersen, C.B.F. et al., Structure of Eef3 and the Mechanism of Transfer RNA Release from the E-Site. Nature (2006)

Release Date

2006-08-09

Peptides

ELONGATION FACTOR 3A: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

ELONGATION FACTOR 3A

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